Clean channel & on-board effects vs Crunch/Lead?

Looking to recreate some 90s Alternative tones like Nirvana's On A Plain, Alice In Chains' Man In a Box & Spoonman by Soundgarden. Kurt liked to use pedals to get his tone, where as Jerry Cantrell will use the amp to get a lot of his distortion.

In your experience, what works best with the Katana?

I have a Katana 100 Mk2.